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De novo assembly and Characterisation of the Transcriptome during seed development, and generation of genic-SSR markers in Peanut (Arachis hypogaea L.)

文献类型： 外文期刊

作者： Zhang, Jianan 1 ; Liang, Shan 3 ; Duan, Jialei 4 ; Wang, Jin 1 ; Chen, Silong 1 ; Cheng, Zengshu 1 ; Zhang, Qiang 1 ; Lia 1 ;

作者机构： 1.Hebei Acad Agr & Forestry Sci, Lab Crop Genet & Breeding Hebei Prov, Inst Food & Oil Crops, Shijiazhuang 050031, Peoples R China

2.Hebei Acad Agr & Forestry Sci, Inst Millet Crops, Natl Millet Improvement Ctr China, Shijiazhuang 050031, Peoples R China

3.Tsinghua Univ, Sch Life Sci, Minist Educ, Prot Sci Lab, Beijing 100084, Peoples R China

4.Chinese Acad Agr Sci, Inst Crop

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2012 年 13 卷

页码：

收录情况： SCI

摘要： Background: The peanut (Arachis hypogaea L.) is an important oilseed crop in tropical and subtropical regions of the world. However, little about the molecular biology of the peanut is currently known. Recently, next-generation sequencing technology, termed RNA-seq, has provided a powerful approach for analysing the transcriptome, and for shedding light on the molecular biology of peanut. Results: In this study, we employed RNA-seq to analyse the transcriptomes of the immature seeds of three different peanut varieties with different oil contents. A total of 26.1-27.2 million paired-end reads with lengths of 100 bp were generated from the three varieties and 59,077 unigenes were assembled with N50 of 823 bp. Based on sequence similarity search with known proteins, a total of 40,100 genes were identified. Among these unigenes, only 8,252 unigenes were annotated with 42 gene ontology (GO) functional categories. And 18,028 unigenes mapped to 125 pathways by searching against the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG). In addition, 3,919 microsatellite markers were developed in the unigene library, and 160 PCR primers of SSR loci were used for validation of the amplification and the polymorphism. Conclusion: We completed a successful global analysis of the peanut transcriptome using RNA-seq, a large number of unigenes were assembled, and almost four thousand SSR primers were developed. These data will facilitate gene discovery and functional genomic studies of the peanut plant. In addition, this study provides insight into the complex transcriptome of the peanut and established a biotechnological platform for future research.

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